Starting phenix.real_space_refine on Sat Jul 4 05:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m49_63619/07_2026/9m49_63619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m49_63619/07_2026/9m49_63619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m49_63619/07_2026/9m49_63619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m49_63619/07_2026/9m49_63619.map" model { file = "/net/cci-nas-00/data/ceres_data/9m49_63619/07_2026/9m49_63619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m49_63619/07_2026/9m49_63619.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Co 2 6.85 5 P 124 5.49 5 S 56 5.16 5 C 11250 2.51 5 N 2993 2.21 5 O 3862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18287 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain: "C" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "E" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "F" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "G" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} Chain: "J" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna3p': 30} Chain: "B" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2705 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "D" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2091 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 2 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CO': 1} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CO': 1} Chain breaks: 1 Time building chain proxies: 4.09, per 1000 atoms: 0.22 Number of scatterers: 18287 At special positions: 0 Unit cell: (120.12, 136.92, 132.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 2 26.99 S 56 16.00 P 124 15.00 O 3862 8.00 N 2993 7.00 C 11250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 683.0 milliseconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3724 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 43 sheets defined 26.4% alpha, 22.0% beta 60 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.715A pdb=" N SER C 308 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 76 Processing helix chain 'E' and resid 129 through 137 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 298 through 310 removed outlier: 4.327A pdb=" N ASP E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 250 through 261 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.632A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.291A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.287A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 266 removed outlier: 5.271A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 322 removed outlier: 7.387A pdb=" N SER A 328 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET A 330 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 341 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 24 through 27 removed outlier: 6.694A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.296A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.238A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AB4, first strand: chain 'C' and resid 263 through 266 removed outlier: 5.298A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP C 282 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N SER C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.427A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.596A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.287A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.287A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.312A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC3, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.984A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 315 through 322 Processing sheet with id=AC5, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.679A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.254A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AC8, first strand: chain 'F' and resid 98 through 99 removed outlier: 8.292A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AD1, first strand: chain 'F' and resid 264 through 266 removed outlier: 6.510A pdb=" N LYS F 276 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER F 293 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR F 278 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL F 291 " --> pdb=" O TYR F 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 315 through 322 removed outlier: 8.442A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.693A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.265A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AD6, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.443A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD8, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.878A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 315 through 322 Processing sheet with id=AE1, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.536A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.298A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AE4, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.371A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AE6, first strand: chain 'D' and resid 263 through 266 removed outlier: 4.562A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP D 282 " --> pdb=" O SER D 288 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N SER D 288 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 319 through 322 591 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4494 1.33 - 1.45: 4118 1.45 - 1.57: 9970 1.57 - 1.69: 244 1.69 - 1.81: 83 Bond restraints: 18909 Sorted by residual: bond pdb=" CA ASP C 310 " pdb=" CB ASP C 310 " ideal model delta sigma weight residual 1.530 1.555 -0.025 1.69e-02 3.50e+03 2.19e+00 bond pdb=" N THR A 340 " pdb=" CA THR A 340 " ideal model delta sigma weight residual 1.455 1.472 -0.018 1.26e-02 6.30e+03 1.94e+00 bond pdb=" C THR A 340 " pdb=" O THR A 340 " ideal model delta sigma weight residual 1.234 1.250 -0.016 1.22e-02 6.72e+03 1.71e+00 bond pdb=" CB ASP C 310 " pdb=" CG ASP C 310 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CB LYS D 149 " pdb=" CG LYS D 149 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.16e+00 ... (remaining 18904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 25594 1.22 - 2.44: 486 2.44 - 3.65: 128 3.65 - 4.87: 12 4.87 - 6.09: 5 Bond angle restraints: 26225 Sorted by residual: angle pdb=" N ILE B 107 " pdb=" CA ILE B 107 " pdb=" C ILE B 107 " ideal model delta sigma weight residual 112.96 108.24 4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" C1' U G 18 " pdb=" N1 U G 18 " pdb=" C2 U G 18 " ideal model delta sigma weight residual 117.70 121.83 -4.13 1.20e+00 6.94e-01 1.19e+01 angle pdb=" CA THR A 340 " pdb=" CB THR A 340 " pdb=" OG1 THR A 340 " ideal model delta sigma weight residual 109.60 104.66 4.94 1.50e+00 4.44e-01 1.09e+01 angle pdb=" C GLN C 309 " pdb=" N ASP C 310 " pdb=" CA ASP C 310 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" O2 U G 18 " pdb=" C2 U G 18 " pdb=" N3 U G 18 " ideal model delta sigma weight residual 122.20 119.97 2.23 7.00e-01 2.04e+00 1.01e+01 ... (remaining 26220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.45: 10831 33.45 - 66.91: 499 66.91 - 100.36: 34 100.36 - 133.81: 0 133.81 - 167.26: 1 Dihedral angle restraints: 11365 sinusoidal: 5599 harmonic: 5766 Sorted by residual: dihedral pdb=" O4' U G 18 " pdb=" C1' U G 18 " pdb=" N1 U G 18 " pdb=" C2 U G 18 " ideal model delta sinusoidal sigma weight residual 200.00 32.74 167.26 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" CA THR A 192 " pdb=" C THR A 192 " pdb=" N TYR A 193 " pdb=" CA TYR A 193 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA THR B 192 " pdb=" C THR B 192 " pdb=" N TYR B 193 " pdb=" CA TYR B 193 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 11362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2105 0.029 - 0.058: 586 0.058 - 0.087: 213 0.087 - 0.116: 179 0.116 - 0.146: 41 Chirality restraints: 3124 Sorted by residual: chirality pdb=" CA ASP C 310 " pdb=" N ASP C 310 " pdb=" C ASP C 310 " pdb=" CB ASP C 310 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE F 79 " pdb=" N ILE F 79 " pdb=" C ILE F 79 " pdb=" CB ILE F 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 79 " pdb=" N ILE A 79 " pdb=" C ILE A 79 " pdb=" CB ILE A 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 3121 not shown) Planarity restraints: 2910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 117 " 0.039 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO B 118 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 310 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C ASP C 310 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP C 310 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 311 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 261 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 262 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.018 5.00e-02 4.00e+02 ... (remaining 2907 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 83 2.60 - 3.17: 14003 3.17 - 3.75: 28270 3.75 - 4.32: 40755 4.32 - 4.90: 64953 Nonbonded interactions: 148064 Sorted by model distance: nonbonded pdb=" O2' U I 18 " pdb="CO CO I 101 " model vdw 2.024 2.960 nonbonded pdb=" O GLU F 304 " pdb=" OG SER F 308 " model vdw 2.224 3.040 nonbonded pdb=" OE1 GLU A 339 " pdb=" O2' A G 19 " model vdw 2.279 3.040 nonbonded pdb=" N GLU D 326 " pdb=" OE1 GLU D 326 " model vdw 2.286 3.120 nonbonded pdb=" OD1 ASN E 45 " pdb=" OG1 THR E 47 " model vdw 2.295 3.040 ... (remaining 148059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 20 or resid 22 through 344)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 20 or resid 22 through 344)) selection = (chain 'E' and (resid 1 through 20 or resid 22 through 344)) selection = (chain 'F' and (resid 1 through 20 or resid 22 through 344)) } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.750 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18909 Z= 0.119 Angle : 0.460 6.092 26225 Z= 0.291 Chirality : 0.040 0.146 3124 Planarity : 0.003 0.060 2910 Dihedral : 16.701 167.263 7641 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.19 % Allowed : 18.43 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1971 helix: 1.35 (0.24), residues: 508 sheet: 1.64 (0.28), residues: 356 loop : -0.02 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 138 TYR 0.008 0.001 TYR B 225 PHE 0.020 0.001 PHE F 302 TRP 0.007 0.001 TRP A 332 HIS 0.002 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (18909) covalent geometry : angle 0.45997 / 0.29 (26225) hydrogen bonds : bond 0.14103 / 9.36 ( 714) hydrogen bonds : angle 6.25207 / 4.39 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.666 Fit side-chains REVERT: A 223 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7254 (tp30) REVERT: A 232 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: A 264 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7589 (tp30) REVERT: A 311 LEU cc_start: 0.7961 (mp) cc_final: 0.7701 (mt) REVERT: A 340 THR cc_start: 0.6596 (OUTLIER) cc_final: 0.6344 (p) REVERT: C 44 GLU cc_start: 0.8540 (tt0) cc_final: 0.8026 (tm-30) REVERT: C 68 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: C 202 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6295 (pt0) REVERT: C 204 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8346 (mttp) REVERT: C 223 GLU cc_start: 0.8045 (tt0) cc_final: 0.7719 (tm-30) REVERT: C 245 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8154 (tt) REVERT: C 319 LYS cc_start: 0.8689 (mttp) cc_final: 0.8468 (mttt) REVERT: E 149 LYS cc_start: 0.8293 (mttt) cc_final: 0.7737 (pmtt) REVERT: E 173 LYS cc_start: 0.8619 (tttp) cc_final: 0.8266 (mtmm) REVERT: E 201 GLN cc_start: 0.7758 (mp10) cc_final: 0.7438 (mp10) REVERT: E 284 GLN cc_start: 0.6580 (tp40) cc_final: 0.6189 (mm110) REVERT: F 204 LYS cc_start: 0.8719 (mttm) cc_final: 0.8357 (mtmt) REVERT: F 296 ASP cc_start: 0.8256 (t0) cc_final: 0.7764 (t0) REVERT: B 254 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7250 (mp) REVERT: B 317 VAL cc_start: 0.6895 (t) cc_final: 0.6637 (p) outliers start: 21 outliers final: 12 residues processed: 163 average time/residue: 0.6156 time to fit residues: 112.5058 Evaluate side-chains 161 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 165 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0570 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0270 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126512 restraints weight = 19463.420| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.16 r_work: 0.3093 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18909 Z= 0.122 Angle : 0.455 6.134 26225 Z= 0.254 Chirality : 0.042 0.164 3124 Planarity : 0.003 0.043 2910 Dihedral : 13.416 165.104 3925 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.84 % Allowed : 16.73 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1971 helix: 1.32 (0.24), residues: 507 sheet: 1.73 (0.28), residues: 332 loop : -0.10 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 138 TYR 0.011 0.001 TYR B 342 PHE 0.015 0.001 PHE F 7 TRP 0.012 0.001 TRP B 332 HIS 0.004 0.001 HIS F 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (18909) covalent geometry : angle 0.45494 / 0.25 (26225) hydrogen bonds : bond 0.04364 / 2.87 ( 714) hydrogen bonds : angle 5.15944 / 3.61 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7449 (tp30) REVERT: A 232 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: A 264 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8062 (tp30) REVERT: A 311 LEU cc_start: 0.8404 (mp) cc_final: 0.8118 (mt) REVERT: A 312 SER cc_start: 0.8705 (p) cc_final: 0.8164 (m) REVERT: C 44 GLU cc_start: 0.8801 (tt0) cc_final: 0.8431 (tm-30) REVERT: C 202 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6751 (pt0) REVERT: C 223 GLU cc_start: 0.8187 (tt0) cc_final: 0.7872 (tm-30) REVERT: C 245 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8479 (tt) REVERT: C 250 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8421 (mp) REVERT: C 319 LYS cc_start: 0.8936 (mttp) cc_final: 0.8725 (mttt) REVERT: E 21 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: E 149 LYS cc_start: 0.8270 (mttt) cc_final: 0.7700 (pmtt) REVERT: E 173 LYS cc_start: 0.8579 (tttp) cc_final: 0.8083 (mttm) REVERT: E 201 GLN cc_start: 0.7758 (mp10) cc_final: 0.7383 (mp10) REVERT: F 204 LYS cc_start: 0.8735 (mttm) cc_final: 0.8366 (mtmt) REVERT: F 232 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.3335 (t80) REVERT: F 296 ASP cc_start: 0.8377 (t0) cc_final: 0.7986 (t0) REVERT: B 254 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7126 (mp) REVERT: B 317 VAL cc_start: 0.6790 (t) cc_final: 0.6563 (p) outliers start: 50 outliers final: 17 residues processed: 187 average time/residue: 0.5775 time to fit residues: 121.5019 Evaluate side-chains 164 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 189 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 186 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 177 ASN B 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.182757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126766 restraints weight = 19568.546| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.11 r_work: 0.3095 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18909 Z= 0.109 Angle : 0.428 4.959 26225 Z= 0.240 Chirality : 0.041 0.143 3124 Planarity : 0.003 0.049 2910 Dihedral : 13.256 163.544 3907 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.67 % Allowed : 17.24 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 1971 helix: 1.31 (0.24), residues: 507 sheet: 1.71 (0.29), residues: 327 loop : -0.14 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 138 TYR 0.010 0.001 TYR A 342 PHE 0.024 0.001 PHE F 213 TRP 0.012 0.001 TRP B 332 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (18909) covalent geometry : angle 0.42847 / 0.24 (26225) hydrogen bonds : bond 0.03870 / 2.53 ( 714) hydrogen bonds : angle 4.93174 / 3.45 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.519 Fit side-chains REVERT: A 223 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7491 (tp30) REVERT: A 232 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: A 264 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8073 (tp30) REVERT: A 311 LEU cc_start: 0.8416 (mp) cc_final: 0.8124 (mt) REVERT: A 312 SER cc_start: 0.8728 (p) cc_final: 0.8191 (m) REVERT: C 44 GLU cc_start: 0.8785 (tt0) cc_final: 0.8407 (tm-30) REVERT: C 202 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6795 (pt0) REVERT: C 223 GLU cc_start: 0.8166 (tt0) cc_final: 0.7853 (tm-30) REVERT: C 250 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8440 (mp) REVERT: C 264 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: C 319 LYS cc_start: 0.8932 (mttp) cc_final: 0.8709 (mttt) REVERT: E 21 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: E 149 LYS cc_start: 0.8216 (mttt) cc_final: 0.7678 (pmtt) REVERT: E 173 LYS cc_start: 0.8578 (tttp) cc_final: 0.8100 (mttm) REVERT: E 181 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7902 (ttpt) REVERT: E 201 GLN cc_start: 0.7767 (mp10) cc_final: 0.7359 (mp10) REVERT: E 284 GLN cc_start: 0.6741 (tp40) cc_final: 0.6494 (mm110) REVERT: F 21 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: F 204 LYS cc_start: 0.8726 (mttm) cc_final: 0.8342 (mtmt) REVERT: F 232 PHE cc_start: 0.4903 (OUTLIER) cc_final: 0.3281 (t80) REVERT: F 296 ASP cc_start: 0.8380 (t0) cc_final: 0.7964 (t0) REVERT: B 254 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7163 (mp) outliers start: 47 outliers final: 19 residues processed: 180 average time/residue: 0.5927 time to fit residues: 119.8071 Evaluate side-chains 161 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 66 optimal weight: 0.0070 chunk 207 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.181537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125605 restraints weight = 19454.624| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.15 r_work: 0.3082 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18909 Z= 0.144 Angle : 0.462 5.078 26225 Z= 0.256 Chirality : 0.043 0.163 3124 Planarity : 0.004 0.054 2910 Dihedral : 13.236 164.123 3903 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.57 % Allowed : 16.90 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 1971 helix: 1.21 (0.24), residues: 507 sheet: 1.55 (0.29), residues: 327 loop : -0.26 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.012 0.001 TYR A 342 PHE 0.023 0.002 PHE F 213 TRP 0.015 0.001 TRP A 332 HIS 0.007 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 (18909) covalent geometry : angle 0.46179 / 0.26 (26225) hydrogen bonds : bond 0.04063 / 2.66 ( 714) hydrogen bonds : angle 4.92708 / 3.44 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.519 Fit side-chains REVERT: A 223 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7460 (tp30) REVERT: A 232 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: A 264 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8097 (tp30) REVERT: A 312 SER cc_start: 0.8767 (p) cc_final: 0.8230 (m) REVERT: C 44 GLU cc_start: 0.8782 (tt0) cc_final: 0.8404 (tm-30) REVERT: C 68 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: C 90 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8174 (mtm-85) REVERT: C 202 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6880 (pt0) REVERT: C 223 GLU cc_start: 0.8132 (tt0) cc_final: 0.7816 (tm-30) REVERT: C 250 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 264 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: E 149 LYS cc_start: 0.8306 (mttt) cc_final: 0.7736 (pmtt) REVERT: E 173 LYS cc_start: 0.8591 (tttp) cc_final: 0.8089 (mttm) REVERT: E 181 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7935 (ttpt) REVERT: E 201 GLN cc_start: 0.7733 (mp10) cc_final: 0.7430 (mp10) REVERT: E 284 GLN cc_start: 0.6759 (tp40) cc_final: 0.6479 (mm110) REVERT: E 321 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7913 (m) REVERT: F 21 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: F 204 LYS cc_start: 0.8712 (mttm) cc_final: 0.8327 (mtmt) REVERT: F 232 PHE cc_start: 0.5001 (OUTLIER) cc_final: 0.3376 (t80) REVERT: F 296 ASP cc_start: 0.8402 (t0) cc_final: 0.7999 (t0) REVERT: B 254 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7213 (mp) REVERT: B 280 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8205 (mt) REVERT: D 104 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8128 (mmm) outliers start: 63 outliers final: 26 residues processed: 191 average time/residue: 0.5190 time to fit residues: 112.1972 Evaluate side-chains 169 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 23 optimal weight: 0.0470 chunk 165 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 163 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 0.0070 chunk 18 optimal weight: 0.6980 chunk 206 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 187 GLN C 201 GLN F 188 GLN D 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127307 restraints weight = 19542.237| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.13 r_work: 0.3120 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18909 Z= 0.080 Angle : 0.400 4.944 26225 Z= 0.225 Chirality : 0.040 0.149 3124 Planarity : 0.003 0.043 2910 Dihedral : 13.149 161.348 3903 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.78 % Allowed : 18.09 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1971 helix: 1.40 (0.24), residues: 507 sheet: 1.64 (0.29), residues: 327 loop : -0.17 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.009 0.001 TYR C 342 PHE 0.022 0.001 PHE F 213 TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00170 / 0.08 (18909) covalent geometry : angle 0.39984 / 0.22 (26225) hydrogen bonds : bond 0.03185 / 2.10 ( 714) hydrogen bonds : angle 4.66935 / 3.26 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.661 Fit side-chains REVERT: A 223 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7418 (tp30) REVERT: A 232 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: A 264 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7937 (tm-30) REVERT: A 311 LEU cc_start: 0.8497 (mp) cc_final: 0.8174 (mt) REVERT: A 312 SER cc_start: 0.8762 (p) cc_final: 0.8232 (m) REVERT: C 44 GLU cc_start: 0.8758 (tt0) cc_final: 0.8369 (tm-30) REVERT: C 46 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8531 (mmmt) REVERT: C 68 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: C 90 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: C 202 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6734 (pt0) REVERT: C 223 GLU cc_start: 0.8217 (tt0) cc_final: 0.7925 (tm-30) REVERT: C 245 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8445 (tt) REVERT: C 250 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8387 (mp) REVERT: C 264 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: E 149 LYS cc_start: 0.8232 (mttt) cc_final: 0.7733 (pmtt) REVERT: E 173 LYS cc_start: 0.8596 (tttp) cc_final: 0.8125 (mttm) REVERT: E 201 GLN cc_start: 0.7752 (mp10) cc_final: 0.7427 (mp10) REVERT: E 284 GLN cc_start: 0.6821 (tp40) cc_final: 0.6521 (mm110) REVERT: E 328 SER cc_start: 0.6724 (OUTLIER) cc_final: 0.6038 (p) REVERT: F 21 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: F 204 LYS cc_start: 0.8728 (mttm) cc_final: 0.8342 (mtmt) REVERT: F 232 PHE cc_start: 0.4939 (OUTLIER) cc_final: 0.3341 (t80) REVERT: F 296 ASP cc_start: 0.8383 (t0) cc_final: 0.8013 (t0) REVERT: B 254 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7215 (mp) outliers start: 49 outliers final: 16 residues processed: 187 average time/residue: 0.5481 time to fit residues: 116.1219 Evaluate side-chains 162 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 128 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 188 GLN F 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127409 restraints weight = 19333.737| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.20 r_work: 0.3094 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18909 Z= 0.102 Angle : 0.417 4.654 26225 Z= 0.231 Chirality : 0.041 0.157 3124 Planarity : 0.003 0.057 2910 Dihedral : 13.127 161.592 3902 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.55 % Allowed : 18.72 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1971 helix: 1.38 (0.24), residues: 507 sheet: 1.60 (0.29), residues: 327 loop : -0.18 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.009 0.001 TYR C 225 PHE 0.023 0.001 PHE F 213 TRP 0.009 0.001 TRP B 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (18909) covalent geometry : angle 0.41679 / 0.23 (26225) hydrogen bonds : bond 0.03397 / 2.24 ( 714) hydrogen bonds : angle 4.67570 / 3.26 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.605 Fit side-chains REVERT: A 223 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7391 (tp30) REVERT: A 232 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: A 264 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8030 (tp30) REVERT: A 312 SER cc_start: 0.8804 (p) cc_final: 0.8280 (m) REVERT: A 340 THR cc_start: 0.8278 (p) cc_final: 0.8063 (p) REVERT: C 44 GLU cc_start: 0.8806 (tt0) cc_final: 0.8404 (tm-30) REVERT: C 46 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8498 (mmmt) REVERT: C 68 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: C 90 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8055 (mtm-85) REVERT: C 202 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6760 (pt0) REVERT: C 223 GLU cc_start: 0.8184 (tt0) cc_final: 0.7865 (tm-30) REVERT: C 245 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8473 (tt) REVERT: C 250 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8435 (mp) REVERT: C 264 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: E 149 LYS cc_start: 0.8229 (mttt) cc_final: 0.7691 (pmtt) REVERT: E 173 LYS cc_start: 0.8588 (tttp) cc_final: 0.8072 (mttm) REVERT: E 201 GLN cc_start: 0.7750 (mp10) cc_final: 0.7418 (mp10) REVERT: E 284 GLN cc_start: 0.6745 (tp40) cc_final: 0.6407 (mm110) REVERT: E 328 SER cc_start: 0.6645 (OUTLIER) cc_final: 0.6011 (p) REVERT: F 21 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: F 187 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7137 (mp10) REVERT: F 204 LYS cc_start: 0.8724 (mttm) cc_final: 0.8324 (mtmt) REVERT: F 232 PHE cc_start: 0.4953 (OUTLIER) cc_final: 0.3350 (t80) REVERT: F 296 ASP cc_start: 0.8402 (t0) cc_final: 0.8007 (t0) REVERT: B 244 GLN cc_start: 0.7556 (tt0) cc_final: 0.7044 (tt0) REVERT: B 254 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7191 (mp) outliers start: 45 outliers final: 19 residues processed: 176 average time/residue: 0.5590 time to fit residues: 111.1994 Evaluate side-chains 168 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 35 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 200 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128932 restraints weight = 19590.722| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.21 r_work: 0.3123 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18909 Z= 0.079 Angle : 0.392 4.949 26225 Z= 0.220 Chirality : 0.040 0.150 3124 Planarity : 0.003 0.049 2910 Dihedral : 13.069 160.231 3902 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.21 % Allowed : 19.34 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1971 helix: 1.43 (0.24), residues: 507 sheet: 1.65 (0.29), residues: 327 loop : -0.14 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.008 0.001 TYR C 342 PHE 0.022 0.001 PHE F 213 TRP 0.008 0.001 TRP B 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 (18909) covalent geometry : angle 0.39230 / 0.22 (26225) hydrogen bonds : bond 0.03019 / 1.99 ( 714) hydrogen bonds : angle 4.57758 / 3.20 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.647 Fit side-chains REVERT: A 149 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7927 (mmmt) REVERT: A 223 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7361 (tp30) REVERT: A 232 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: A 264 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8025 (tp30) REVERT: A 311 LEU cc_start: 0.8530 (mp) cc_final: 0.8194 (mt) REVERT: A 312 SER cc_start: 0.8788 (p) cc_final: 0.8265 (m) REVERT: C 44 GLU cc_start: 0.8776 (tt0) cc_final: 0.8403 (tm-30) REVERT: C 68 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: C 202 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6752 (pt0) REVERT: C 223 GLU cc_start: 0.8219 (tt0) cc_final: 0.7893 (tm-30) REVERT: C 245 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8418 (tt) REVERT: C 250 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8375 (mp) REVERT: C 264 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: E 21 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: E 149 LYS cc_start: 0.8165 (mttt) cc_final: 0.7743 (pmtt) REVERT: E 173 LYS cc_start: 0.8603 (tttp) cc_final: 0.8117 (mttm) REVERT: E 201 GLN cc_start: 0.7766 (mp10) cc_final: 0.7421 (mp10) REVERT: E 284 GLN cc_start: 0.6783 (tp40) cc_final: 0.6447 (mm110) REVERT: E 328 SER cc_start: 0.6657 (OUTLIER) cc_final: 0.6065 (p) REVERT: F 21 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: F 187 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7170 (mp10) REVERT: F 204 LYS cc_start: 0.8704 (mttm) cc_final: 0.8316 (mtmt) REVERT: F 232 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.3358 (t80) REVERT: F 296 ASP cc_start: 0.8395 (t0) cc_final: 0.8021 (t0) REVERT: B 244 GLN cc_start: 0.7570 (tt0) cc_final: 0.7121 (tt0) REVERT: B 254 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7218 (mp) outliers start: 39 outliers final: 20 residues processed: 175 average time/residue: 0.5308 time to fit residues: 105.2875 Evaluate side-chains 169 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 177 ASN F 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127829 restraints weight = 19440.975| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.20 r_work: 0.3097 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18909 Z= 0.101 Angle : 0.415 4.964 26225 Z= 0.230 Chirality : 0.041 0.153 3124 Planarity : 0.003 0.047 2910 Dihedral : 13.054 161.019 3902 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.33 % Allowed : 19.57 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1971 helix: 1.39 (0.24), residues: 507 sheet: 1.61 (0.29), residues: 322 loop : -0.18 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 138 TYR 0.009 0.001 TYR C 225 PHE 0.026 0.001 PHE F 213 TRP 0.008 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (18909) covalent geometry : angle 0.41492 / 0.23 (26225) hydrogen bonds : bond 0.03305 / 2.17 ( 714) hydrogen bonds : angle 4.61053 / 3.22 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.609 Fit side-chains REVERT: A 149 LYS cc_start: 0.8147 (mmpt) cc_final: 0.7937 (mmpt) REVERT: A 223 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7378 (tp30) REVERT: A 232 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: A 264 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8063 (tp30) REVERT: A 311 LEU cc_start: 0.8511 (mp) cc_final: 0.8175 (mt) REVERT: A 312 SER cc_start: 0.8783 (p) cc_final: 0.8281 (m) REVERT: C 44 GLU cc_start: 0.8794 (tt0) cc_final: 0.8407 (tm-30) REVERT: C 46 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8511 (mmmt) REVERT: C 68 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: C 90 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.7586 (mtm-85) REVERT: C 202 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6745 (pt0) REVERT: C 223 GLU cc_start: 0.8217 (tt0) cc_final: 0.7897 (tm-30) REVERT: C 245 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8474 (tt) REVERT: C 250 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8401 (mp) REVERT: C 264 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: E 21 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: E 149 LYS cc_start: 0.8172 (mttt) cc_final: 0.7708 (pmtt) REVERT: E 173 LYS cc_start: 0.8598 (tttp) cc_final: 0.8068 (mttm) REVERT: E 201 GLN cc_start: 0.7734 (mp10) cc_final: 0.7383 (mp10) REVERT: E 284 GLN cc_start: 0.6740 (tp40) cc_final: 0.6389 (mm110) REVERT: E 328 SER cc_start: 0.6588 (OUTLIER) cc_final: 0.6027 (p) REVERT: F 21 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: F 187 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7170 (mp10) REVERT: F 204 LYS cc_start: 0.8725 (mttm) cc_final: 0.8318 (mtmt) REVERT: F 232 PHE cc_start: 0.4949 (OUTLIER) cc_final: 0.3337 (t80) REVERT: F 296 ASP cc_start: 0.8416 (t0) cc_final: 0.7995 (t0) REVERT: B 244 GLN cc_start: 0.7548 (tt0) cc_final: 0.7088 (tt0) REVERT: B 254 LEU cc_start: 0.7449 (mm) cc_final: 0.7139 (mp) outliers start: 41 outliers final: 22 residues processed: 172 average time/residue: 0.5620 time to fit residues: 108.7040 Evaluate side-chains 166 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 157 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 187 GLN C 201 GLN F 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.182725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126772 restraints weight = 19387.101| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.08 r_work: 0.3103 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18909 Z= 0.096 Angle : 0.409 5.434 26225 Z= 0.227 Chirality : 0.040 0.155 3124 Planarity : 0.003 0.044 2910 Dihedral : 13.027 160.942 3900 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 19.57 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1971 helix: 1.39 (0.24), residues: 507 sheet: 1.60 (0.29), residues: 322 loop : -0.19 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 138 TYR 0.009 0.001 TYR C 225 PHE 0.026 0.001 PHE F 213 TRP 0.009 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (18909) covalent geometry : angle 0.40894 / 0.23 (26225) hydrogen bonds : bond 0.03199 / 2.10 ( 714) hydrogen bonds : angle 4.59780 / 3.22 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.537 Fit side-chains REVERT: A 223 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7385 (tp30) REVERT: A 232 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: A 264 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7906 (tm-30) REVERT: A 311 LEU cc_start: 0.8589 (mp) cc_final: 0.8254 (mt) REVERT: A 312 SER cc_start: 0.8766 (p) cc_final: 0.8290 (m) REVERT: C 44 GLU cc_start: 0.8779 (tt0) cc_final: 0.8421 (tm-30) REVERT: C 46 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8526 (mmmt) REVERT: C 68 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: C 90 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.7874 (mtm-85) REVERT: C 202 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6849 (pt0) REVERT: C 223 GLU cc_start: 0.8226 (tt0) cc_final: 0.7934 (tm-30) REVERT: C 245 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8501 (tt) REVERT: C 250 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8439 (mp) REVERT: C 264 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: E 21 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: E 149 LYS cc_start: 0.8186 (mttt) cc_final: 0.7795 (pmtt) REVERT: E 173 LYS cc_start: 0.8597 (tttp) cc_final: 0.8140 (mttm) REVERT: E 201 GLN cc_start: 0.7764 (mp10) cc_final: 0.7418 (mp10) REVERT: E 284 GLN cc_start: 0.6818 (tp40) cc_final: 0.6503 (mm110) REVERT: E 328 SER cc_start: 0.6655 (OUTLIER) cc_final: 0.6134 (p) REVERT: F 21 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: F 187 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7210 (mp10) REVERT: F 204 LYS cc_start: 0.8703 (mttm) cc_final: 0.8324 (mtmt) REVERT: F 232 PHE cc_start: 0.5056 (OUTLIER) cc_final: 0.3434 (t80) REVERT: F 296 ASP cc_start: 0.8417 (t0) cc_final: 0.8036 (t0) REVERT: B 254 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7314 (mp) outliers start: 41 outliers final: 23 residues processed: 172 average time/residue: 0.5306 time to fit residues: 103.0124 Evaluate side-chains 173 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 11 optimal weight: 0.0020 chunk 204 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 145 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.0370 overall best weight: 0.9270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 177 ASN F 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.182392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127201 restraints weight = 19443.683| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.21 r_work: 0.3083 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18909 Z= 0.104 Angle : 0.419 5.378 26225 Z= 0.232 Chirality : 0.041 0.155 3124 Planarity : 0.003 0.068 2910 Dihedral : 13.021 161.325 3900 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.33 % Allowed : 19.63 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1971 helix: 1.38 (0.24), residues: 507 sheet: 1.56 (0.29), residues: 322 loop : -0.21 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.009 0.001 TYR C 225 PHE 0.025 0.001 PHE F 213 TRP 0.009 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 (18909) covalent geometry : angle 0.41917 / 0.23 (26225) hydrogen bonds : bond 0.03326 / 2.18 ( 714) hydrogen bonds : angle 4.61682 / 3.23 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.612 Fit side-chains REVERT: A 149 LYS cc_start: 0.8135 (mmpt) cc_final: 0.7933 (mmmt) REVERT: A 223 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7379 (tp30) REVERT: A 232 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: A 264 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8038 (tp30) REVERT: A 312 SER cc_start: 0.8778 (p) cc_final: 0.8313 (m) REVERT: C 44 GLU cc_start: 0.8792 (tt0) cc_final: 0.8392 (tm-30) REVERT: C 46 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8508 (mmmt) REVERT: C 68 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: C 90 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8221 (mtm-85) REVERT: C 202 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6756 (pt0) REVERT: C 223 GLU cc_start: 0.8180 (tt0) cc_final: 0.7857 (tm-30) REVERT: C 245 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8472 (tt) REVERT: C 250 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8451 (mp) REVERT: C 264 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: E 149 LYS cc_start: 0.8163 (mttt) cc_final: 0.7709 (pmtt) REVERT: E 173 LYS cc_start: 0.8588 (tttp) cc_final: 0.8060 (mttm) REVERT: E 201 GLN cc_start: 0.7736 (mp10) cc_final: 0.7382 (mp10) REVERT: E 284 GLN cc_start: 0.6754 (tp40) cc_final: 0.6395 (mm110) REVERT: E 328 SER cc_start: 0.6582 (OUTLIER) cc_final: 0.6087 (p) REVERT: F 21 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: F 187 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7145 (mp10) REVERT: F 204 LYS cc_start: 0.8715 (mttm) cc_final: 0.8304 (mtmt) REVERT: F 232 PHE cc_start: 0.4944 (OUTLIER) cc_final: 0.3352 (t80) REVERT: F 296 ASP cc_start: 0.8424 (t0) cc_final: 0.8004 (t0) REVERT: B 191 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7925 (mp0) REVERT: B 254 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7142 (mp) outliers start: 41 outliers final: 24 residues processed: 171 average time/residue: 0.5583 time to fit residues: 107.6874 Evaluate side-chains 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 142 optimal weight: 30.0000 chunk 158 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125477 restraints weight = 19375.849| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.01 r_work: 0.3083 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18909 Z= 0.126 Angle : 0.449 6.569 26225 Z= 0.247 Chirality : 0.042 0.160 3124 Planarity : 0.004 0.068 2910 Dihedral : 13.036 162.805 3900 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.21 % Allowed : 19.68 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 1971 helix: 1.27 (0.24), residues: 508 sheet: 1.49 (0.29), residues: 333 loop : -0.28 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 138 TYR 0.013 0.001 TYR F 193 PHE 0.028 0.002 PHE F 213 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (18909) covalent geometry : angle 0.44907 / 0.25 (26225) hydrogen bonds : bond 0.03628 / 2.37 ( 714) hydrogen bonds : angle 4.70881 / 3.30 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6722.40 seconds wall clock time: 115 minutes 0.07 seconds (6900.07 seconds total)